how do alignment programs perform on sequencing data with varying qualities and from repetitive regions如何校准程序执行对测序数据的不同品质和重复的区域.pdfVIP

Yu et al. BioData Mining 2012, 5:6 /content/5/1/6 BioData Mining RESEARCH Open Access How do alignment programs perform on sequencing data with varying qualities and from repetitive regions? 1 2,3 4 2 5 3 Xiaoqing Yu , Kishore Guda , Joseph Willis , Martina Veigl , Zhenghe Wang , Sanford Markowitz , Mark D Adams5 and Shuying Sun1,2* Abstract Background: Next-generation sequencing technologies generate a significant number of short reads that are utilized to address a variety of biological questions. However, quite often, sequencing reads tend to have low quality at the 3’ end and are generated from the repetitive regions of a genome. It is unclear how different alignment programs perform under these different cases. In order to investigate this question, we use both real data and simulated data with the above issues to evaluate the performance of four commonly used algorithms: SOAP2, Bowtie, BWA, and Novoalign. Methods: The performance of different alignment algorithms are measured in terms of concordance between any pair of aligners (for real sequencing data without known truth) and the accuracy of simulated read alignment. Results: Our results show that, for sequencing data with reads that have relatively good quality or that have had low quality bases trimmed off, all four alignment programs perform similarly. We have also demonstrated that trimming off low quality ends markedly increases the number of aligned reads and improves the consistency among different aligners as well, especially for low quality data. However, Novoalign is more sensitive to the improvement of data quality. Trimming off low quality ends significantly incr